tbuckley/cabot-search huggingface dataset:
Histogram of Oriented Gradients meet deep learning: A novel multi-task deep network for 2D surgical image semantic segmentation
Authors: Binod Bhattarai, Ronast Subedi, Rebati Raman Gaire, Eduard Vazquez, Danail Stoyanov
Journal: Medical Image Analysis (2023)

We present our novel deep multi-task learning method for medical image segmentation. Existing multi-task methods demand ground truth annotations for both the primary and auxiliary tasks. Contrary to it, we propose to generate the pseudo-labels of an auxiliary task in an unsupervised manner. To generate the pseudo-labels, we leverage Histogram of Oriented Gradients (HOGs), one of the most widely used and powerful hand-crafted features for detection. Together with the ground truth semantic segmentation masks for the primary task and pseudo-labels for the auxiliary task, we learn the parameters of the deep network to minimize the loss of both the primary task and the auxiliary task jointly. We employed our method on two powerful and widely used semantic segmentation networks: UNet and U2Net to train in a multi-task setup. To validate our hypothesis, we performed experiments on two different medical image segmentation data sets. From the extensive quantitative and qualitative results, we observe that our method consistently improves the performance compared to the counter-part method. Moreover, our method is the winner of FetReg Endovis Sub-challenge on Semantic Segmentation organised in conjunction with MICCAI 2021. Code and implementation details are available at:https://github.com/thetna/medical_image_segmentation.
Osteopontin mediation of disturbed flow–induced endothelial mesenchymal transition through CD44 is a novel mechanism of neointimal hyperplasia in arteriovenous fistulae for hemodialysis access
Authors: Chi-Jen Chang, Ying-Ju Lai, Ying-Chang Tung, Lung-Sheng Wu, Lung-An Hsu, Chi-Nan Tseng, Gwo-Jyh Chang, Kai-Chien Yang, Yung-Hsin Yeh
Journal: Kidney International (2023)
Radiation to all macroscopic sites of tumor permits greater systemic antitumor response to in situ vaccination
Authors: Peter M Carlson, Ravi B Patel, Jen Birstler, Matthew Rodriquez, Claire Sun, Amy K Erbe, Amber M Bates, Ian Marsh, Joseph Grudzinski, Reinier Hernandez, Alexander A Pieper, Arika S Feils, Alexander L Rakhmilevich, Jamey P Weichert, Bryan P Bednarz, Paul M Sondel, Zachary S Morris
Journal: Journal for ImmunoTherapy of Cancer (2023)

Background The antitumor effects of external beam radiation therapy (EBRT) are mediated, in part, by an immune response. We have reported that a single fraction of 12 Gy EBRT combined with intratumoral anti-GD2 hu14.18-IL2 immunocytokine (IC) generates an effective in situ vaccine (ISV) against GD2-positive murine tumors. This ISV is effective in eradicating single tumors with sustained immune memory; however, it does not generate an adequate abscopal response against macroscopic distant tumors. Given the immune-stimulatory capacity of radiation therapy (RT), we hypothesized that delivering RT to all sites of disease would augment systemic antitumor responses to ISV. Methods We used a syngeneic B78 murine melanoma model consisting of a ‘primary’ flank tumor and a contralateral smaller ‘secondary’ flank tumor, treated with 12 Gy EBRT and intratumoral IC immunotherapy to the primary and additional EBRT to the secondary tumor. As a means of delivering RT to all sites of disease, both known and occult, we also used a novel alkylphosphocholine analog, NM600, conjugated to 90 Y as a targeted radionuclide therapy (TRT). Tumor growth, overall survival, and cause of death were measured. Flow cytometry was used to evaluate immune population changes in both tumors. Results Abscopal effects of local ISV were amplified by delivering as little as 2–6 Gy of EBRT to the secondary tumor. When the primary tumor ISV regimen was delivered in mice receiving 12 Gy EBRT to the secondary tumor, we observed improved overall survival and more disease-free mice with immune memory compared with either ISV or 12 Gy EBRT alone. Similarly, TRT combined with ISV resulted in improved overall survival and a trend towards reduced tumor growth rates when compared with either treatment alone. Using flow cytometry, we identified an influx of CD8 + T cells with a less exhausted phenotype in both the ISV-targeted primary and the distant secondary tumor following the combination of secondary tumor EBRT or TRT with primary tumor ISV. Conclusions We report a novel use for low-dose RT, not as a direct antitumor modality but as an immunomodulator capable of driving and expanding antitumor immunity against metastatic tumor sites following ISV.
Pathophysiology of obesity and its associated diseases
Authors: Xin Jin, Tingting Qiu, Li Li, Rilei Yu, Xiguang Chen, Changgui Li, Christopher G. Proud, Tao Jiang
Journal: Acta Pharmaceutica Sinica B (2023)

The occurrence of obesity has increased across the whole world. Many epidemiological studies have indicated that obesity strongly contributes to the development of cancer, cardiovascular diseases, type 2 diabetes, liver diseases and other disorders, accounting for a heavy burden on the public and on health-care systems every year. Excess energy uptake induces adipocyte hypertrophy, hyperplasia and formation of visceral fat in other non-adipose tissues to evoke cardiovascular disease, liver diseases. Adipose tissue can also secrete adipokines and inflammatory cytokines to affect the local microenvironment, induce insulin resistance, hyperglycemia, and activate associated inflammatory signaling pathways. This further exacerbates the development and progression of obesity-associated diseases. Although some progress in the treatment of obesity has been achieved in preclinical and clinical studies, the progression and pathogenesis of obesity-induced diseases are complex and unclear. We still need to understand their links to better guide the treatment of obesity and associated diseases. In this review, we review the links between obesity and other diseases, with a view to improve the future management and treatment of obesity and its co-morbidities.
A systematic study of nano-based fibrous systems: Diagnostic and therapeutic approaches for dementia control
Authors: Maryam Chehrehgosha, Kamyar Khoshnevisan, Hassan Maleki, Hadi Baharifar, Amir Mohammad Meftah, Sayed Mahmoud Sajjadi-Jazi, Farshad Sharifi
Journal: Ageing Research Reviews (2023)
The Efficacy of Defocus Incorporated Multiple Segments Lenses in Slowing Myopia Progression
Authors: Jiaxin Liu, Yiqiu Lu, Dan Huang, Jiwen Yang, Chunlei Fan, Chunmei Chen, Jianhua Li, Qinqin Wang, Shan Li, Baolin Jiang, Hongyan Jiang, Xiaoning Li, Zhikuan Yang, Weizhong Lan
Journal: Ophthalmology (2023)
A systematic review of trials currently investigating therapeutic modalities for post-acute COVID-19 syndrome and registered on WHO International Clinical Trials Platform
Authors: Nader A. Fawzy, Bader Abou Shaar, Rand M. Taha, Tarek Z. Arabi, Belal N. Sabbah, Mohamad S. Alkodaymi, Osama A. Omrani, Tariq Makhzoum, Najwa E. Almahfoudh, Qasem A. Al-Hammad, Wed Hejazi, Yasin Obeidat, Naden Osman, Khaled M. Al-Kattan, Elie F. Berbari, Imad M. Tleyjeh
Journal: Clinical Microbiology and Infection (2023)
Minimally Invasive Thymectomy Could Be Attempted for Locally Advanced Thymic Malignancies: A Real-World Study With Propensity Score-Matched Analysis
Authors: Zhitao Gu, Xiuxiu Hao, Yuan Liu, Ning Xu, Xuefei Zhang, Bofei Li, Teng Mao, Wentao Fang
Journal: Journal of Thoracic Oncology (2023)
Comparative Safety of Biologic Agents in Patients With Inflammatory Bowel Disease With Active or Recent Malignancy: A Multi-Center Cohort Study
Authors: Ariela K. Holmer, Jiyu Luo, Kirk B. Russ, Sarah Park, Jeong Yun Yang, Furkan Ertem, Jeffrey Dueker, Vu Nguyen, Simon Hong, Cameron Zenger, Jordan E. Axelrad, Anthony Sofia, Jessica C. Petrov, Badr Al-Bawardy, David I. Fudman, Ernesto Llano, Joseph Dailey, Sushrut Jangi, Nidah Khakoo, Oriana M. Damas, Edward L. Barnes, Frank I. Scott, Ryan C. Ungaro, Siddharth Singh
Journal: Clinical Gastroenterology and Hepatology (2023)
Prevalence and Characteristics of Nonalcoholic Fatty Liver Disease and Fibrosis in People Living With HIV Monoinfection: A Systematic Review and Meta-analysis
Authors: Markos Kalligeros, Athanasios Vassilopoulos, Fadi Shehadeh, Stephanos Vassilopoulos, Ingrid Lazaridou, Eleftherios Mylonakis, Kittichai Promrat, Jack R. Wands
Journal: Clinical Gastroenterology and Hepatology (2023)
Outcomes of invasive melanoma of the head and neck treated with Mohs micrographic surgery – A multicenter study
Authors: Brandon T. Beal, Jeremy Udkoff, Leora Aizman, Jeremy Etzkorn, John A. Zitelli, Christopher J. Miller, Thuzar M. Shin, Joseph F. Sobanko, David G. Brodland
Journal: Journal of the American Academy of Dermatology (2023)
Issue Information
Authors: Arif Kamal, Ted Gansler, Keith Delman, Esmeralda Buchanan, Jin Kim, Jasmine Hargrave-Thomas, Meredith Krebs-Smith Wiley, Subhalakshmi Venkattu, Gini Fleming, Frederick Greene, Ahmedin Jemal, Cathy Meade, Kevin Oeffinger, Alpa Patel, Nancy Perrier, Charles Thomas, Andrew Vickers, Mike Fillon, Ilana Cass, Jill Roberts, Philip Benoit, Nicholas Jensen 17 Cancer, Rebecca Siegel, Kimberly Miller, Nikita Sandeep, Wagle Mbbs, Jemal Mha, Jason Foster, Chunmeng Zhang, Shahyan Rehman, Prateek Sharma, ; Richard Alexander, Rajat Thawani, Myung Kim, Zizhen Feng, Malinda West, Nicholas Taflin, ; Kyaw, Zin Thein, Ryan Li, Mathew Geltzeiler, Nancy Lee, ; Clifton, David Fuller, Jennifer Grandis, Charalampos Floudas, Michael Heinrich, Ehab Hanna, Ravi Chandra
Journal: CA A Cancer Journal for Clinicians (2023)

No abstract is available for this article.
Infection-responsive long-term antibacterial bone plates for open fracture therapy
Authors: Lujiao Zhang, Yurun Yang, Yan-Hua Xiong, Yu-Qing Zhao, Zongpeng Xiu, Hui-Min Ren, Kai Zhang, Shun Duan, Ying Chen, Fu-Jian Xu
Journal: Bioactive Materials (2023)

The infections in open fracture induce high morbidity worldwide. Thus, developing efficient anti-infective orthopedic devices is of great significance. In this work, we designed a kind of infection-responsive long-term antibacterial bone plates. Through a facile and flexible volatilization method, a multi-aldehyde polysaccharide derivative, oxidized sodium alginate, was crosslinked with multi-amino compounds, gentamycin and gelatin, to fabricate a uniform coating on Ti bone plates via Schiff base reaction, which was followed by a secondary crosslinking process by glutaraldehyde. The double-crosslinked coating was stable under normal condition, and could responsively release gentamycin by the triggering of the acidic microenvironment caused by bacterial metabolism, owning to the pH-responsiveness of imine structure. The thickness of the coating was ranging from 22.0 μm to 63.6 μm. The coated bone plates (Ti-GOGs) showed infection-triggered antibacterial properties (>99%) and high biocompatibility. After being soaked for five months, it still possessed efficient antibacterial ability, showing its sustainable antibacterial performance. The in vivo anti-infection ability was demonstrated by an animal model of infection after fracture fixation (IAFF). At the early stage of IAFF, Ti-GOGs could inhibit the bacterial infection (>99%). Subsequently, Ti-GOGs could promote recovery of fracture of IAFF. This work provides a convenient and universal strategy for fabrication of various antibacterial orthopedic devices, which is promising to prevent and treat IAFF.
Targeting the IL4 receptor with MDNA55 in patients with recurrent glioblastoma: Results of a phase IIb trial
Authors: John H Sampson, Achal Singh Achrol, Manish K Aghi, Krystof Bankiewicz, Martin Bexon, Steven Brem, Andrew Brenner, Chandtip Chandhasin, Sajeel Chowdhary, Melissa Coello, Benjamin M Ellingson, John R Floyd, Seunggu Han, Santosh Kesari, Yael Mardor, Fahar Merchant, Nina Merchant, Dina Randazzo, Michael Vogelbaum, Frank Vrionis, Eva Wembacher-Schroeder, Miroslaw Zabek, Nicholas Butowski
Journal: Neuro-Oncology (2023)

Abstract Background MDNA55 is an interleukin 4 receptor (IL4R)-targeting toxin in development for recurrent GBM, a universally fatal disease. IL4R is overexpressed in GBM as well as cells of the tumor microenvironment. High expression of IL4R is associated with poor clinical outcomes. Methods MDNA55-05 is an open-label, single-arm phase IIb study of MDNA55 in recurrent GBM (rGBM) patients with an aggressive form of GBM (de novo GBM, IDH wild-type, and nonresectable at recurrence) on their 1st or 2nd recurrence. MDNA55 was administered intratumorally as a single dose treatment (dose range of 18 to 240 ug) using convection-enhanced delivery (CED) with up to 4 stereo-tactically placed catheters. It was co-infused with a contrast agent (Gd-DTPA, Magnevist®) to assess distribution in and around the tumor margins. The flow rate of each catheter did not exceed 10μL/min to ensure that the infusion duration did not exceed 48 h. The primary endpoint was mOS, with secondary endpoints determining the effects of IL4R status on mOS and PFS. Results MDNA55 showed an acceptable safety profile at doses up to 240 μg. In all evaluable patients (n = 44) mOS was 11.64 months (80% one-sided CI 8.62, 15.02) and OS-12 was 46%. A subgroup (n = 32) consisting of IL4R High and IL4R Low patients treated with high-dose MDNA55 (&amp;gt;180 ug) showed the best benefit with mOS of 15 months, OS-12 of 55%. Based on mRANO criteria, tumor control was observed in 81% (26/32), including those patients who exhibited pseudo-progression (15/26). Conclusions MDNA55 demonstrated tumor control and promising survival and may benefit rGBM patients when treated at high-dose irrespective of IL4R expression level. Trial Registration: Clinicaltrials.gov NCT02858895.
CholecTriplet2021: A benchmark challenge for surgical action triplet recognition
Authors: Chinedu Innocent Nwoye, Deepak Alapatt, Tong Yu, Armine Vardazaryan, Fangfang Xia, Zixuan Zhao, Tong Xia, Fucang Jia, Yuxuan Yang, Hao Wang, Derong Yu, Guoyan Zheng, Xiaotian Duan, Neil Getty, Ricardo Sanchez-Matilla, Maria Robu, Li Zhang, Huabin Chen, Jiacheng Wang, Liansheng Wang, Bokai Zhang, Beerend Gerats, Sista Raviteja, Rachana Sathish, Rong Tao, Satoshi Kondo, Winnie Pang, Hongliang Ren, Julian Ronald Abbing, Mohammad Hasan Sarhan, Sebastian Bodenstedt, Nithya Bhasker, Bruno Oliveira, Helena R. Torres, Li Ling, Finn Gaida, Tobias Czempiel, João L. Vilaça, Pedro Morais, Jaime Fonseca, Ruby Mae Egging, Inge Nicole Wijma, Chen Qian, Guibin Bian, Zhen Li, Velmurugan Balasubramanian, Debdoot Sheet, Imanol Luengo, Yuanbo Zhu, Shuai Ding, Jakob-Anton Aschenbrenner, Nicolas Elini van der Kar, Mengya Xu, Mobarakol Islam, Lalithkumar Seenivasan, Alexander Jenke, Danail Stoyanov, Didier Mutter, Pietro Mascagni, Barbara Seeliger, Cristians Gonzalez, Nicolas Padoy
Journal: Medical Image Analysis (2023)
Ultralow Background Near‐Infrared Fluorophores with Dual‐Channel Intraoperative Imaging Capability
Authors: Kai Bao, Molly Tully, Kevin Cardenas, Haoran Wang, Surbhi Srinivas, Jiyun Rho, Ok Hwa Jeon, Jason Dinh, Shinya Yokomizo, Rose McDonnell, Atsushi Yamashita, Satoshi Kashiwagi, Homan Kang, Hyun Koo Kim, Hak Soo Choi
Journal: Advanced Healthcare Materials (2023)

Two of the most pressing challenges facing bioimaging are nonspecific uptake of intravenously administered contrast agents and incomplete elimination of unbound targeted agents from the body. Designing a targeted contrast agent that shows fast clearance from background tissues and eventually the body after complete targeting is key to the success of image-guided interventions. Here, this work describes the development of renally clearable near-infrared contrast agents and their potential use for dual-channel image-guided tumor targeting. cRGD-ZW800-PEG (800 nm channel) and ZW700-PEG (700 nm channel) are able to visualize tumor margins and tumor vasculature simultaneously and respectively. These targeted agents show rapid elimination from the bloodstream, followed by renal clearance, which together significantly lower off-target background signals and potential toxicity. To demonstrate its applicability, this multispectral imaging is performed in various tumor-bearing animal models including lung cancer, pancreatic neuroendocrine tumors, breast, and ovarian cancer.
Intronic SNP - rs9288953 Of Suppressor Molecule Btla Confers Susceptibility To B-Cell Chronic Lymphocytic Leukemia
Authors: Anna Partyka, Anna Tomkiewicz, Edyta Pawlak-Adamska, Olga Grzybowska–Izydorczyk, Ewa Lech–Maranda, Agnieszka Bojarska–Junak, Iwona Hus, Tadeusz Robak, Jacek M. Rolinski, Lidia Karabon
Journal: Blood (2013)
Candidate diagnostic biomarkers for neurodevelopmental disorders in children and adolescents: a systematic review
Authors: Samuele Cortese, Marco Solmi, Giorgia Michelini, Alessio Bellato, Christina Blanner, Andrea Canozzi, Luis Eudave, Luis C. Farhat, Mikkel Højlund, Ole Köhler‐Forsberg, Douglas Teixeira Leffa, Christopher Rohde, Gonzalo Salazar de Pablo, Giovanni Vita, Rikke Wesselhoeft, Joanna Martin, Sarah Baumeister, Natali S. Bozhilova, Christina O. Carlisi, Virginia Carter Leno, Dorothea L. Floris, Nathalie E. Holz, Eline J. Kraaijenvanger, Seda Sacu, Isabella Vainieri, Giovanni Ostuzzi, Corrado Barbui, Christoph U. Correll
Journal: World Psychiatry (2023)

Neurodevelopmental disorders - including attention-deficit/hyperactivity disorder (ADHD), autism spectrum disorder, communication disorders, intellectual disability, motor disorders, specific learning disorders, and tic disorders - manifest themselves early in development. Valid, reliable and broadly usable biomarkers supporting a timely diagnosis of these disorders would be highly relevant from a clinical and public health standpoint. We conducted the first systematic review of studies on candidate diagnostic biomarkers for these disorders in children and adolescents. We searched Medline and Embase + Embase Classic with terms relating to biomarkers until April 6, 2022, and conducted additional targeted searches for genome-wide association studies (GWAS) and neuroimaging or neurophysiological studies carried out by international consortia. We considered a candidate biomarker as promising if it was reported in at least two independent studies providing evidence of sensitivity and specificity of at least 80%. After screening 10,625 references, we retained 780 studies (374 biochemical, 203 neuroimaging, 133 neurophysiological and 65 neuropsychological studies, and five GWAS), including a total of approximately 120,000 cases and 176,000 controls. While the majority of the studies focused simply on associations, we could not find any biomarker for which there was evidence - from two or more studies from independent research groups, with results going into the same direction - of specificity and sensitivity of at least 80%. Other important metrics to assess the validity of a candidate biomarker, such as positive predictive value and negative predictive value, were infrequently reported. Limitations of the currently available studies include mostly small sample size, heterogeneous approaches and candidate biomarker targets, undue focus on single instead of joint biomarker signatures, and incomplete accounting for potential confounding factors. Future multivariable and multi-level approaches may be best suited to find valid candidate biomarkers, which will then need to be validated in external, independent samples and then, importantly, tested in terms of feasibility and cost-effectiveness, before they can be implemented in daily clinical practice.
New insights from the last decade of research in psychiatric genetics: discoveries, challenges and clinical implications
Authors: Ole A. Andreassen, Guy F.L. Hindley, Oleksandr Frei, Olav B. Smeland
Journal: World Psychiatry (2023)

Psychiatric genetics has made substantial progress in the last decade, providing new insights into the genetic etiology of psychiatric disorders, and paving the way for precision psychiatry, in which individual genetic profiles may be used to personalize risk assessment and inform clinical decision‐making. Long recognized to be heritable, recent evidence shows that psychiatric disorders are influenced by thousands of genetic variants acting together. Most of these variants are commonly occurring, meaning that every individual has a genetic risk to each psychiatric disorder, from low to high. A series of large‐scale genetic studies have discovered an increasing number of common and rare genetic variants robustly associated with major psychiatric disorders. The most convincing biological interpretation of the genetic findings implicates altered synaptic function in autism spectrum disorder and schizophrenia. However, the mechanistic understanding is still incomplete. In line with their extensive clinical and epidemiological overlap, psychiatric disorders appear to exist on genetic continua and share a large degree of genetic risk with one another. This provides further support to the notion that current psychiatric diagnoses do not represent distinct pathogenic entities, which may inform ongoing attempts to reconceptualize psychiatric nosology. Psychiatric disorders also share genetic influences with a range of behavioral and somatic traits and diseases, including brain structures, cognitive function, immunological phenotypes and cardiovascular disease, suggesting shared genetic etiology of potential clinical importance. Current polygenic risk score tools, which predict individual genetic susceptibility to illness, do not yet provide clinically actionable information. However, their precision is likely to improve in the coming years, and they may eventually become part of clinical practice, stressing the need to educate clinicians and patients about their potential use and misuse. This review discusses key recent insights from psychiatric genetics and their possible clinical applications, and suggests future directions.